Hi Dan,
Yes, I was using ptraj. Thank you for pointing this out.
I tried cpptraj with this input:
trajin traj.mdcrd 1 5 1
trajout test.mdcrd nobox
center :1-10 mass origin
closest 20 :1-10 first closestout closestout.dat
There was no output produced, not even test.mdcrd. With ptraj, at least the
correct test.mdcrd was produced.
Am I missing anything for cpptraj please?
Thanks!
Qiong
On Thu, Apr 12, 2012 at 7:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Are you using ptraj? The 'closestout' keyword is only implemented in
> cpptraj.
>
> -Dan
>
> On Apr 12, 2012, at 5:30 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I am using ambertools1.5 and encountered a problem when using the closest
> > command. The script I am using is as follows:
> >
> > trajin traj.mdcrd 1 5 1
> > trajout test.mdcrd nobox
> > solvent byname WAT
> > center :1-10 mass origin
> > closest 20 :1-10 first closestout closestout.dat
> >
> > With this I can obtain the trajectory output test.mdcrd where the 20
> > closest waters to residue 1-10 are selected. But no *closestout.dat* file
> > was produced.
> > In the manual it says that " If “closestout” is specified information on
> > the closest solvent molecules will be print to
> > <filename> with format:
> > Frame Molecule Distance FirstAtom# "
> >
> > Could anybody please give me some hint on what might be wrong here
> please?
> > Thanks!
> >
> > And if the closestout.dat is produced, what exact content is in this file
> > please? Will the RESID or AtomID of the closest solvent be given as
> > FirstAtom# please?
> >
> > Qiong
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Apr 12 2012 - 19:00:03 PDT
